Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva-Cañas, José L.; Vlasova, Anna; Marcet-Houben, Marina|||0000-0003-4838-187X; Martínez-Cruz, Begoña; Cheng, Jade Yu; Prieto, Pablo; Quesada, Víctor|||0000-0002-8398-3457; Quilez, Javier|||0000-0002-0108-2672; Li, Gang|||0000-0001-8399-7771; García, Francisca|||0000-0002-2141-7628; Rubio-Camarillo, M.; Frias, Leonor; Ribeca, Paolo; Capella-Gutiérrez, Salvador; Rodríguez, J. M.; Câmara, F.; Lowy, Ernesto; Cozzuto, Luca|||0000-0003-3194-8892; Erb, Ionas|||0000-0002-2331-9714; Tress, M. L.; Rodriguez-Ales, J. L.; Ruiz-Orera, J.; Reverter, F.; Casas-Marce, M.; Soriano, L.; Arango, Javier R.; Derdak, Sophia; Galán, Beatriz; Blanc, Julie; Gut, Marta|||0000-0002-4063-7159; Lorente-Galdos, Belen|||0000-0001-5390-2452; Andrés Nieto, Marta|||0000-0001-5267-0039; López-Otín, C.; Valencia, A.; Gut, Ivo|||0000-0001-7219-632X; García, J. L.; Guigó, Roderic|||0000-0002-5738-4477; Murphy, W. J.; Ruiz Herrera Moreno, Aurora|||0000-0003-3868-6151; Marquès i Bonet, Tomàs|||0000-0002-5597-3075; Roma, Guglielmo; Notredame, C.; Mailund, Thomas; Albà, M. Mar; Gabaldón, Toni|||0000-0003-0019-1735; Alioto, Tyler Scott|||0000-0002-2960-5420; Godoy, José A.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a...

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Autores:	Abascal, Federico, Corvelo, André, Cruz, Fernando, Villanueva-Cañas, José L., Vlasova, Anna, Marcet-Houben, Marina\|\|\|0000-0003-4838-187X, Martínez-Cruz, Begoña, Cheng, Jade Yu, Prieto, Pablo, Quesada, Víctor\|\|\|0000-0002-8398-3457, Quilez, Javier\|\|\|0000-0002-0108-2672, Li, Gang\|\|\|0000-0001-8399-7771, García, Francisca\|\|\|0000-0002-2141-7628, Rubio-Camarillo, M., Frias, Leonor, Ribeca, Paolo, Capella-Gutiérrez, Salvador, Rodríguez, J. M., Câmara, F., Lowy, Ernesto, Cozzuto, Luca\|\|\|0000-0003-3194-8892, Erb, Ionas\|\|\|0000-0002-2331-9714, Tress, M. L., Rodriguez-Ales, J. L., Ruiz-Orera, J., Reverter, F., Casas-Marce, M., Soriano, L., Arango, Javier R., Derdak, Sophia, Galán, Beatriz, Blanc, Julie, Gut, Marta\|\|\|0000-0002-4063-7159, Lorente-Galdos, Belen\|\|\|0000-0001-5390-2452, Andrés Nieto, Marta\|\|\|0000-0001-5267-0039, López-Otín, C., Valencia, A., Gut, Ivo\|\|\|0000-0001-7219-632X, García, J. L., Guigó, Roderic\|\|\|0000-0002-5738-4477, Murphy, W. J., Ruiz Herrera Moreno, Aurora\|\|\|0000-0003-3868-6151, Marquès i Bonet, Tomàs\|\|\|0000-0002-5597-3075, Roma, Guglielmo, Notredame, C., Mailund, Thomas, Albà, M. Mar, Gabaldón, Toni\|\|\|0000-0003-0019-1735, Alioto, Tyler Scott\|\|\|0000-0002-2960-5420, Godoy, José A.
Tipo de recurso:	artículo
Fecha de publicación:	2016
País:	España
Institución:	Universitat Autònoma de Barcelona
Repositorio:	Dipòsit Digital de Documents de la UAB
Idioma:	inglés
OAI Identifier:	oai:ddd.uab.cat:225199
Acceso en línea:	https://ddd.uab.cat/record/225199 https://dx.doi.org/urn:doi:10.1186/s13059-016-1090-1
Access Level:	acceso abierto
Palabra clave:	Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx

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repository_id_str
spelling	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynxAbascal, FedericoCorvelo, AndréCruz, FernandoVillanueva-Cañas, José L.Vlasova, AnnaMarcet-Houben, Marina\|\|\|0000-0003-4838-187XMartínez-Cruz, BegoñaCheng, Jade YuPrieto, PabloQuesada, Víctor\|\|\|0000-0002-8398-3457Quilez, Javier\|\|\|0000-0002-0108-2672Li, Gang\|\|\|0000-0001-8399-7771García, Francisca\|\|\|0000-0002-2141-7628Rubio-Camarillo, M.Frias, LeonorRibeca, PaoloCapella-Gutiérrez, SalvadorRodríguez, J. M.Câmara, F.Lowy, ErnestoCozzuto, Luca\|\|\|0000-0003-3194-8892Erb, Ionas\|\|\|0000-0002-2331-9714Tress, M. L.Rodriguez-Ales, J. L.Ruiz-Orera, J.Reverter, F.Casas-Marce, M.Soriano, L.Arango, Javier R.Derdak, SophiaGalán, BeatrizBlanc, JulieGut, Marta\|\|\|0000-0002-4063-7159Lorente-Galdos, Belen\|\|\|0000-0001-5390-2452Andrés Nieto, Marta\|\|\|0000-0001-5267-0039López-Otín, C.Valencia, A.Gut, Ivo\|\|\|0000-0001-7219-632XGarcía, J. L.Guigó, Roderic\|\|\|0000-0002-5738-4477Murphy, W. J.Ruiz Herrera Moreno, Aurora\|\|\|0000-0003-3868-6151Marquès i Bonet, Tomàs\|\|\|0000-0002-5597-3075Roma, GuglielmoNotredame, C.Mailund, ThomasAlbà, M. MarGabaldón, Toni\|\|\|0000-0003-0019-1735Alioto, Tyler Scott\|\|\|0000-0002-2960-5420Godoy, José A.Conservation genomicsGenetic diversityInbreedingGenetic driftLynxBackground: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. - Results: ce generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. -Conclusions: the genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species. 22016-01-0120162016-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/225199https://dx.doi.org/urn:doi:10.1186/s13059-016-1090-1reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengEuropean Commission https://doi.org/10.13039/501100000780 264125Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 PT13/0001/0021Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2012-0208Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2012-0262open accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2251992026-06-06T12:50:31Z
dc.title.none.fl_str_mv	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
title	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
spellingShingle	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx Abascal, Federico Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx
title_short	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
title_full	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
title_fullStr	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
title_full_unstemmed	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
title_sort	Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
dc.creator.none.fl_str_mv	Abascal, Federico Corvelo, André Cruz, Fernando Villanueva-Cañas, José L. Vlasova, Anna Marcet-Houben, Marina\|\|\|0000-0003-4838-187X Martínez-Cruz, Begoña Cheng, Jade Yu Prieto, Pablo Quesada, Víctor\|\|\|0000-0002-8398-3457 Quilez, Javier\|\|\|0000-0002-0108-2672 Li, Gang\|\|\|0000-0001-8399-7771 García, Francisca\|\|\|0000-0002-2141-7628 Rubio-Camarillo, M. Frias, Leonor Ribeca, Paolo Capella-Gutiérrez, Salvador Rodríguez, J. M. Câmara, F. Lowy, Ernesto Cozzuto, Luca\|\|\|0000-0003-3194-8892 Erb, Ionas\|\|\|0000-0002-2331-9714 Tress, M. L. Rodriguez-Ales, J. L. Ruiz-Orera, J. Reverter, F. Casas-Marce, M. Soriano, L. Arango, Javier R. Derdak, Sophia Galán, Beatriz Blanc, Julie Gut, Marta\|\|\|0000-0002-4063-7159 Lorente-Galdos, Belen\|\|\|0000-0001-5390-2452 Andrés Nieto, Marta\|\|\|0000-0001-5267-0039 López-Otín, C. Valencia, A. Gut, Ivo\|\|\|0000-0001-7219-632X García, J. L. Guigó, Roderic\|\|\|0000-0002-5738-4477 Murphy, W. J. Ruiz Herrera Moreno, Aurora\|\|\|0000-0003-3868-6151 Marquès i Bonet, Tomàs\|\|\|0000-0002-5597-3075 Roma, Guglielmo Notredame, C. Mailund, Thomas Albà, M. Mar Gabaldón, Toni\|\|\|0000-0003-0019-1735 Alioto, Tyler Scott\|\|\|0000-0002-2960-5420 Godoy, José A.
author	Abascal, Federico
author_facet	Abascal, Federico Corvelo, André Cruz, Fernando Villanueva-Cañas, José L. Vlasova, Anna Marcet-Houben, Marina\|\|\|0000-0003-4838-187X Martínez-Cruz, Begoña Cheng, Jade Yu Prieto, Pablo Quesada, Víctor\|\|\|0000-0002-8398-3457 Quilez, Javier\|\|\|0000-0002-0108-2672 Li, Gang\|\|\|0000-0001-8399-7771 García, Francisca\|\|\|0000-0002-2141-7628 Rubio-Camarillo, M. Frias, Leonor Ribeca, Paolo Capella-Gutiérrez, Salvador Rodríguez, J. M. Câmara, F. Lowy, Ernesto Cozzuto, Luca\|\|\|0000-0003-3194-8892 Erb, Ionas\|\|\|0000-0002-2331-9714 Tress, M. L. Rodriguez-Ales, J. L. Ruiz-Orera, J. Reverter, F. Casas-Marce, M. Soriano, L. Arango, Javier R. Derdak, Sophia Galán, Beatriz Blanc, Julie Gut, Marta\|\|\|0000-0002-4063-7159 Lorente-Galdos, Belen\|\|\|0000-0001-5390-2452 Andrés Nieto, Marta\|\|\|0000-0001-5267-0039 López-Otín, C. Valencia, A. Gut, Ivo\|\|\|0000-0001-7219-632X García, J. L. Guigó, Roderic\|\|\|0000-0002-5738-4477 Murphy, W. J. Ruiz Herrera Moreno, Aurora\|\|\|0000-0003-3868-6151 Marquès i Bonet, Tomàs\|\|\|0000-0002-5597-3075 Roma, Guglielmo Notredame, C. Mailund, Thomas Albà, M. Mar Gabaldón, Toni\|\|\|0000-0003-0019-1735 Alioto, Tyler Scott\|\|\|0000-0002-2960-5420 Godoy, José A.
author_role	author
author2	Corvelo, André Cruz, Fernando Villanueva-Cañas, José L. Vlasova, Anna Marcet-Houben, Marina\|\|\|0000-0003-4838-187X Martínez-Cruz, Begoña Cheng, Jade Yu Prieto, Pablo Quesada, Víctor\|\|\|0000-0002-8398-3457 Quilez, Javier\|\|\|0000-0002-0108-2672 Li, Gang\|\|\|0000-0001-8399-7771 García, Francisca\|\|\|0000-0002-2141-7628 Rubio-Camarillo, M. Frias, Leonor Ribeca, Paolo Capella-Gutiérrez, Salvador Rodríguez, J. M. Câmara, F. Lowy, Ernesto Cozzuto, Luca\|\|\|0000-0003-3194-8892 Erb, Ionas\|\|\|0000-0002-2331-9714 Tress, M. L. Rodriguez-Ales, J. L. Ruiz-Orera, J. Reverter, F. Casas-Marce, M. Soriano, L. Arango, Javier R. Derdak, Sophia Galán, Beatriz Blanc, Julie Gut, Marta\|\|\|0000-0002-4063-7159 Lorente-Galdos, Belen\|\|\|0000-0001-5390-2452 Andrés Nieto, Marta\|\|\|0000-0001-5267-0039 López-Otín, C. Valencia, A. Gut, Ivo\|\|\|0000-0001-7219-632X García, J. L. Guigó, Roderic\|\|\|0000-0002-5738-4477 Murphy, W. J. Ruiz Herrera Moreno, Aurora\|\|\|0000-0003-3868-6151 Marquès i Bonet, Tomàs\|\|\|0000-0002-5597-3075 Roma, Guglielmo Notredame, C. Mailund, Thomas Albà, M. Mar Gabaldón, Toni\|\|\|0000-0003-0019-1735 Alioto, Tyler Scott\|\|\|0000-0002-2960-5420 Godoy, José A.
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
dc.subject.none.fl_str_mv	Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx
topic	Conservation genomics Genetic diversity Inbreeding Genetic drift Lynx
description	Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. - Results: ce generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. -Conclusions: the genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
publishDate	2016
dc.date.none.fl_str_mv	2 2016-01-01 2016 2016-01-01
dc.type.none.fl_str_mv	Article http://purl.org/coar/resource_type/c_6501 VoR http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://ddd.uab.cat/record/225199 https://dx.doi.org/urn:doi:10.1186/s13059-016-1090-1
url	https://ddd.uab.cat/record/225199 https://dx.doi.org/urn:doi:10.1186/s13059-016-1090-1
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.relation.none.fl_str_mv	European Commission https://doi.org/10.13039/501100000780 264125 Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 PT13/0001/0021 Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2012-0208 Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 SEV-2012-0262
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	open access http://purl.org/coar/access_right/c_abf2 https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.source.none.fl_str_mv	reponame:Dipòsit Digital de Documents de la UAB instname:Universitat Autònoma de Barcelona
instname_str	Universitat Autònoma de Barcelona
reponame_str	Dipòsit Digital de Documents de la UAB
collection	Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

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